WIP: install ok. need to invoke program

Dockerfile

@@ -163,7 +163,8 @@ RUN wget https://github.com/bxlab/metaWRAP/archive/refs/tags/v1.3.tar.gz \
 
 ENV PATH="${PATH}:/quackers_tools/metaWRAP-1.3/bin"
 
-RUN apt-get install -y git-all \
+RUN apt-get update \
+&& apt-get install -y git-all \
 && git clone https://github.com/lh3/bwa.git \
 && cd bwa \
 && make
@@ -354,11 +355,13 @@ ENV PATH="${PATH}:/quackers_tools/megahit/bin"
 RUN apt-get update \
 && apt-get install -y ncbi-blast+ git libglpk-dev r-base-core exonerate bedtools barrnap bc parallel curl libcurl4-openssl-dev libssl-dev libsbml5-dev bc
 WORKDIR /quackers_tools/gapseq
+
 RUN apt-get update \
 && apt-get install -y r-base
 RUN apt-get update \
 && apt-get install curl
-RUN wget https://compsysbio.org/quackers_deps/gapseq_r_install.R
+RUN apt-get update \
+&& wget https://compsysbio.org/quackers_deps/gapseq_r_install.R
 
 RUN Rscript gapseq_r_install.R
 WORKDIR /quackers_pipe
@@ -386,5 +389,11 @@ RUN wget https://raw.githubusercontent.com/ParkinsonLab/quackers/v1.0.2/modded_s
 RUN wget https://raw.githubusercontent.com/ParkinsonLab/quackers/v1.0.2/modded_scripts/merge_cutup_clustering.py
 RUN wget https://raw.githubusercontent.com/ParkinsonLab/quackers/v1.0.2/modded_scripts/print_comment.py
 
-
+WORKDIR /quackers_pipe/gapseq
+RUN wget https://cran.r-project.org/src/contrib/Archive/sybil/sybil_2.2.0.tar.gz
+RUN wget https://cran.r-project.org/src/contrib/Archive/sybilSBML/sybilSBML_3.1.2.tar.gz
+R CMD INSTALL sybil_2.2.0.tar.gz
+R CMD INSTALL sybilSBML_3.1.2.tar.gz
+rm sybil_2.2.0.tar.gz
+rm sybilSBML_3.1.2.tar.gz
 CMD ["bash"]

dev_notes.txt

@@ -1,3 +1,8 @@
+Sept 18, 2024:
+--------------------------------------------------------------------
+Contig resolution has been nerf'd using assumptions.  Now installing GapSeq <R tool> and integrating to Quackers
+
+
 Sept 12, 2024:
 ---------------------------------------------